Blind tests of RNA nearest-neighbor energy prediction (Q28828288)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

title

Blind tests of RNA nearest-neighbor energy prediction (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

nearest neighbour algorithm

18 March 2020

main subject

1 reference

1 reference

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18 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

Fang-Chieh Chou

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

Wipapat Kladwang

series ordinal

1 reference

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18 March 2020

language of work or name

English

0 references

publication date

8 July 2016

1 reference

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18 March 2020

number of pages

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

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18 March 2020

volume

113

1 reference

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18 March 2020

issue

1 reference

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18 March 2020

page(s)

8430-8435

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

RNA-guided human genome engineering via Cas9

18 March 2020

cites work

1 reference

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Multiplex genome engineering using CRISPR/Cas systems

16 March 2017

1 reference

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16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Stability and structure of RNA duplexes containing isoguanosine and isocytidine

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

The contribution of pseudouridine to stabilities and structure of RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Effect of sodium ions on RNA duplex stability

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Atomic accuracy in predicting and designing noncanonical RNA structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Free energy profile of RNA hairpins: a molecular dynamics simulation study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Thermodynamic characterization of naturally occurring RNA tetraloops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

RNA challenges for computational chemists

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Water and ion binding around RNA and DNA (C,G) oligomers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4968729

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1523335113

Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1523335113

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1523335113

Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1523335113

Pseudouridine in a new era of RNA modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1523335113

Thermodynamics of three-way multibranch loops in RNA

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27402765

12 December 2020

inferred from PubMed ID database lookup

Absorption and Optical Rotatory Dispersion of Seven Trinucleoside Diphosphates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27402765

12 December 2020

inferred from PubMed ID database lookup

Predicting thermodynamic properties of RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27402765

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1073/PNAS.1523335113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

0 references

1 reference

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18 March 2020

PubMed publication ID

27402765

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27402765%20AND%20SRC:MED&resulttype=core&format=json